png loses alpha on gltf export
Sorry, this is a known bug, a regression.  Issue #425 details it, and a fix is in the works in #506.  Sometime in the next few days it should start working again, after that PR gets merged.

Also, even after the missing alpha channel gets fixed, you'll still have to specifically enable blending mode per-material.  This is done in the "Settings" panel of an Eevee material, "Blend Mode" should be set to "Alpha Blend".